Cilia and flagella have attracted tremendous attention in recent years as research demonstrated crucial roles for these organelles in coordinating a number of physiologically and developmentally important signaling pathways, including the platelet-derived growth factor receptor (PDGFR) alpha, Sonic hedgehog, polycystin, and Wnt pathways. In addition, the realization that defective assembly or function of cilia can cause a plethora of diseases and developmental defects ("ciliopathies") has increased focus on the mechanisms by which these antenna-like, microtubular structures assemble. Ciliogenesis is a complex, multistep process that is tightly coordinated with cell cycle progression and differentiation. The ciliary axoneme is extended from a modified centriole, the basal body, which migrates to and docks onto the apical plasma membrane early in ciliogenesis as cells enter growth arrest. The ciliary axoneme is elongated via intraflagellar transport (IFT), a bidirectional transport system that tracks along the polarized microtubules of the axoneme, and which is required for assembly of almost all cilia and flagella. Here, we provide an overview of ciliogenesis with particular emphasis on the molecular mechanisms and functions of IFT. In addition to a general, up-to-date description of IFT, we discuss mechanisms by which proteins are selectively targeted to the ciliary compartment, with special focus on the ciliary transition zone. Finally, we briefly review the role of IFT in cilia-mediated signaling, including how IFT is directly involved in moving signaling moieties into and out of the ciliary compartment.